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faops.c
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faops.c
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#define _GNU_SOURCE
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <stdint.h> // uint_fast8_t etc
#include <unistd.h> // getopt
#include <getopt.h> // http://stackoverflow.com/questions/22575940/getopt-not-included-implicit-declaration-of-function-getopt
// create dir
#ifdef __MINGW32__
#include <direct.h>
#else
#include <sys/stat.h>
#include <sys/types.h>
#endif
// kseq support gzipped files
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
// khash init
#include "khash.h"
// **str2int** will be the name of HASH throughout the whole file
// key is string, value is int
KHASH_MAP_INIT_STR(str2int, int)
// **str2str** will be the name of HASH throughout the whole file
// key is string, value is string
KHASH_MAP_INIT_STR(str2str, char*)
// this macro doesn't work on a decayed pointer,
// e.g. array name passed to a subroutine
#define ArraySize(a) (sizeof(a) / sizeof((a)[0]))
enum {
BUFFER_SIZE = 2 ^ 16,
BUFFER_SIZE_LONG = 2 ^ 32
};
enum {
T_BASE_VAL = 0,
U_BASE_VAL = 0,
C_BASE_VAL = 1,
A_BASE_VAL = 2,
G_BASE_VAL = 3,
N_BASE_VAL = 4
};
// Standard IUB/IUPAC Nucleic Acid Codes
// Code => Nucleic Acid(s)
// A => Adenine
// C => Cytosine
// G => Guanine
// T => Thymine
// U => Uracil
// M => A or C (amino)
// R => A or G (purine)
// W => A or T (weak)
// S => C or G (strong)
// Y => C or T (pyrimidine)
// K => G or T (keto)
// V => A or C or G
// H => A or C or T
// D => A or G or T
// B => C or G or T
// N => A or G or C or T (any)
int nt_val[256];
void init_nt_val() {
for (int i = 0; i < ArraySize(nt_val); i++) {
nt_val[i] = -1;
}
nt_val['t'] = nt_val['T'] = T_BASE_VAL;
nt_val['u'] = nt_val['U'] = U_BASE_VAL;
nt_val['c'] = nt_val['C'] = C_BASE_VAL;
nt_val['a'] = nt_val['A'] = A_BASE_VAL;
nt_val['g'] = nt_val['G'] = G_BASE_VAL;
nt_val['m'] = nt_val['M'] = N_BASE_VAL;
nt_val['r'] = nt_val['R'] = N_BASE_VAL;
nt_val['w'] = nt_val['W'] = N_BASE_VAL;
nt_val['s'] = nt_val['S'] = N_BASE_VAL;
nt_val['y'] = nt_val['Y'] = N_BASE_VAL;
nt_val['k'] = nt_val['K'] = N_BASE_VAL;
nt_val['v'] = nt_val['V'] = N_BASE_VAL;
nt_val['h'] = nt_val['H'] = N_BASE_VAL;
nt_val['d'] = nt_val['D'] = N_BASE_VAL;
nt_val['b'] = nt_val['B'] = N_BASE_VAL;
nt_val['n'] = nt_val['N'] = N_BASE_VAL;
}
//$seq =~ tr/ACGTMRWSYKVHDBNacgtmrwsykvhdbn-/TGCAKYWSRMBDHVNtgcakywsrmbdhvn-/;
int nt_comp[256];
void init_nt_comp() {
memset(nt_comp, '\0', sizeof(nt_comp));
nt_comp[' '] = ' ';
nt_comp['-'] = '-';
nt_comp['A'] = 'T';
nt_comp['C'] = 'G';
nt_comp['G'] = 'C';
nt_comp['T'] = 'A';
nt_comp['M'] = 'K';
nt_comp['R'] = 'Y';
nt_comp['W'] = 'W';
nt_comp['S'] = 'S';
nt_comp['Y'] = 'R';
nt_comp['K'] = 'M';
nt_comp['V'] = 'B';
nt_comp['H'] = 'D';
nt_comp['D'] = 'H';
nt_comp['B'] = 'V';
nt_comp['N'] = 'N';
nt_comp['U'] = 'A';
nt_comp['a'] = 't';
nt_comp['c'] = 'g';
nt_comp['g'] = 'c';
nt_comp['t'] = 'a';
nt_comp['m'] = 'k';
nt_comp['r'] = 'y';
nt_comp['w'] = 'w';
nt_comp['s'] = 's';
nt_comp['y'] = 'r';
nt_comp['k'] = 'm';
nt_comp['v'] = 'b';
nt_comp['h'] = 'd';
nt_comp['d'] = 'h';
nt_comp['b'] = 'v';
nt_comp['n'] = 'n';
nt_comp['u'] = 'a';
}
void reverse_str(char *str, long length) {
long half_length = (length >> 1);
char *end = str + length;
char c;
while (--half_length >= 0) {
c = *str;
*str++ = *--end;
*end = c;
}
}
void complement_str(char *str, long length) {
for (long i = 0; i < length; ++i) {
str[i] = nt_comp[(int) str[i]];
}
}
// for qsort
static int compare_long_desc(const void *a, const void *b) {
long arg1 = *(const long *) a;
long arg2 = *(const long *) b;
if (arg1 < arg2) return 1;
if (arg1 > arg2) return -1;
return 0;
}
// count Ns in sequence
int count_n(char *str, long length) {
int n_count = 0;
for (int i = 0; i < length; i++) {
int base_val = nt_val[(int) (str[i])];
if (base_val == N_BASE_VAL) {
n_count++;
}
}
return n_count;
}
int is_n(char nt) {
return (nt_val[(int) nt] == N_BASE_VAL || nt_val[(int) nt] == -1);
}
// convert IUPAC ambiguous codes to 'N'
char convert_n(char nt) {
if (is_n(nt)) {
return 'N';
} else {
return nt;
}
}
// convert to Upper case
char convert_U(char nt) {
return (char) toupper(nt);
}
// https://biowize.wordpress.com/2013/03/05/using-kseq-h-with-stdin/
// stream_in
FILE *source_in(char *file) {
FILE *stream;
if (strcmp(file, "stdin") == 0) {
stream = stdin;
} else {
if ((stream = fopen(file, "r")) == NULL) {
fprintf(stderr, "Cannot open input file [%s]\n", file);
exit(1);
}
}
return stream;
}
// stream_out
FILE *source_out(char *file) {
FILE *stream;
if (strcmp(file, "stdout") == 0) {
stream = stdout;
} else {
if ((stream = fopen(file, "w")) == NULL) {
fprintf(stderr, "Cannot open output file [%s]\n", file);
exit(1);
}
}
return stream;
}
int fa_count(int argc, char *argv[]) {
if (argc == optind) {
fprintf(stderr,
"\n"
"faops count - count base statistics in FA file(s).\n"
"usage:\n"
" faops count <in.fa> [more_files.fa]\n"
"\n");
exit(1);
}
unsigned long total_length = 0;
unsigned long total_base_count[5] = {0};
printf("#seq\tlen\tA\tC\tG\tT\tN");
printf("\n");
for (int f = 1; f < argc; ++f) {
gzFile fp = gzdopen(fileno(source_in(argv[f])), "r");
kseq_t *seq = kseq_init(fp);
while (kseq_read(seq) >= 0) {
unsigned long length = 0;
unsigned long base_count[5] = {0};
for (int i = 0; i < seq->seq.l; i++) {
int base_val = nt_val[(int) (seq->seq.s[i])];
if (base_val >= 0 && base_val <= 4) {
length++;
base_count[base_val]++;
}
}
printf("%s\t%lu\t%lu\t%lu\t%lu\t%lu\t%lu", seq->name.s, length,
base_count[A_BASE_VAL], base_count[C_BASE_VAL],
base_count[G_BASE_VAL], base_count[T_BASE_VAL],
base_count[N_BASE_VAL]);
printf("\n");
total_length += length;
for (int i = 0; i < ArraySize(base_count); i++)
total_base_count[i] += base_count[i];
}
kseq_destroy(seq);
gzclose(fp);
}
printf("total\t%lu\t%lu\t%lu\t%lu\t%lu\t%lu", total_length,
total_base_count[A_BASE_VAL], total_base_count[C_BASE_VAL],
total_base_count[G_BASE_VAL], total_base_count[T_BASE_VAL],
total_base_count[N_BASE_VAL]);
printf("\n");
return 0;
}
int fa_size(int argc, char *argv[]) {
if (argc == optind) {
fprintf(stderr,
"\n"
"faops size - count total bases in FA file(s).\n"
"usage:\n"
" faops size <in.fa> [more_files.fa]\n"
"\n"
"in.fa == stdin means reading from stdin\n"
"\n");
exit(1);
}
for (int f = 1; f < argc; ++f) {
gzFile fp = gzdopen(fileno(source_in(argv[f])), "r");
kseq_t *seq = kseq_init(fp);
while (kseq_read(seq) >= 0) {
printf("%s\t%lu", seq->name.s, seq->seq.l);
printf("\n");
}
kseq_destroy(seq);
gzclose(fp);
}
return 0;
}
int fa_masked(int argc, char *argv[]) {
int flag_g = 0;
int option = 0;
while ((option = getopt(argc, argv, "g")) != -1) {
switch (option) {
case 'g':
flag_g = 1;
break;
default:
fprintf(stderr, "Unsupported option\n");
exit(1);
}
}
if (argc == optind) {
fprintf(
stderr,
"\n"
"faops masked - Masked (or gaps) regions in fasta files\n"
"usage:\n"
" faops masked [options] <in.fa> [more_files.fa]\n"
"\n"
"options:\n"
" -g only record regions of N/n\n"
"\n"
"in.fa == stdin means reading from stdin\n"
"\n");
exit(1);
}
for (int f = optind; f < argc; ++f) {
gzFile fp = gzdopen(fileno(source_in(argv[f])), "r");
kseq_t *seq = kseq_init(fp);
while (kseq_read(seq) >= 0) {
int begin = -1, end = -1;
for (int i = 0; i < seq->seq.l; i++) {
if (flag_g
? is_n(seq->seq.s[i])
: (is_n(seq->seq.s[i]) || islower(seq->seq.s[i]))) {
if (begin == -1) {
begin = i, end = i;
} else {
end = i;
}
} else if (begin != -1) {
if (begin == end) {
printf("%s:%u\n", seq->name.s, begin + 1);
} else {
printf("%s:%u-%u\n", seq->name.s, begin + 1, end + 1);
}
// reset
begin = -1, end = -1;
}
}
// last region
if (begin != -1) {
if (begin == end) {
printf("%s:%u\n", seq->name.s, begin + 1);
} else {
printf("%s:%u-%u\n", seq->name.s, begin + 1, end + 1);
}
}
}
kseq_destroy(seq);
gzclose(fp);
}
return 0;
}
int fa_frag(int argc, char *argv[]) {
int option = 0, line = 80;
while ((option = getopt(argc, argv, "l:")) != -1) {
switch (option) {
case 'l':
line = atoi(optarg);
break;
default:
fprintf(stderr, "Unsupported option\n");
exit(1);
}
}
if (optind + 4 > argc || !isdigit(argv[optind + 1][0]) ||
!isdigit(argv[optind + 2][0])) {
fprintf(stderr,
"\n"
"faops frag - Extract a piece of DNA from a FA file.\n"
"usage:\n"
" faops frag [options] <in.fa> <start> <end> <out.fa>\n"
"\n"
"options:\n"
" -l INT sequence line length [%d]\n"
"\n"
"in.fa == stdin means reading from stdin\n"
"out.fa == stdout means writing to stdout\n"
"\n",
line);
exit(1);
}
char *file_in = argv[optind];
int start = atoi(argv[optind + 1]);
int end = atoi(argv[optind + 2]);
char *file_out = argv[optind + 3];
if (start > end) {
fprintf(stderr, "start [%d] > end [%d]\n", start, end);
exit(1);
}
gzFile fp = gzdopen(fileno(source_in(file_in)), "r");
kseq_t *seq = kseq_init(fp);
FILE *stream_out = source_out(file_out);
char seq_name[512];
int is_first = 1;
while (kseq_read(seq) >= 0) {
if (!is_first) {
fprintf(stderr, "More than one sequence in %s, just using first\n",
file_in);
break;
}
if (end > seq->seq.l) {
fprintf(stderr, "%s only has %zu bases\n", seq->name.s,
seq->seq.l);
exit(1);
}
if (start < end) {
sprintf(seq_name, "%s:%d-%d", seq->name.s, start, end);
} else {
sprintf(seq_name, "%s:%d", seq->name.s, start);
}
fprintf(stream_out, ">%s\n", seq_name);
for (int i = 0; i < end - start + 1; i++) {
if (line != 0 && i != 0 && (i % line) == 0) {
fputc('\n', stream_out);
}
fputc(seq->seq.s[i + start - 1], stream_out);
}
fputc('\n', stream_out);
is_first = 0;
}
kseq_destroy(seq);
gzclose(fp);
if (strcmp(file_out, "stdout") != 0) {
fclose(stream_out);
}
return 0;
}
int fa_rc(int argc, char *argv[]) {
int flag_n = 0, flag_r = 0, flag_c = 0;
char *fn_list = "";
int option = 0, line = 80;
while ((option = getopt(argc, argv, "nrcf:l:")) != -1) {
switch (option) {
case 'n':
flag_n = 1;
break;
case 'r':
flag_r = 1;
break;
case 'c':
flag_c = 1;
break;
case 'f':
fn_list = strdup(optarg);
break;
case 'l':
line = atoi(optarg);
break;
default:
fprintf(stderr, "Unsupported option\n");
exit(1);
}
}
char *prefix = flag_n ? "" : (flag_r ? "R_" : (flag_c ? "C_" : "RC_"));
if (optind + 2 > argc) {
fprintf(stderr,
"\n"
"faops rc - Reverse complement a FA file.\n"
"usage:\n"
" faops rc [options] <in.fa> <out.fa>\n"
"\n"
"options:\n"
" -n keep name identical (don't prepend RC_)\n"
" -r just Reverse, prepends R_\n"
" -c just Complement, prepends C_\n"
" -f STR only RC sequences in this list.file\n"
" -l INT sequence line length [%d]\n"
"\n"
"in.fa == stdin means reading from stdin\n"
"out.fa == stdout means writing to stdout\n"
"\n",
line);
exit(1);
}
// Read list.file to a hash table
khash_t(str2int) *hash;
hash = kh_init(str2int);
int serial = 0; // serials in list.file
if (strcmp(fn_list, "") != 0) {
FILE *fp_list;
if ((fp_list = fopen(fn_list, "r")) == NULL) {
fprintf(stderr, "Cannot open list file [%s]\n", fn_list);
exit(1);
}
int ret; // return value from hashing
int buf_size = BUFFER_SIZE;
char buf[buf_size]; // buffers for names in list.file
while (fscanf(fp_list, "%s\n", buf) == 1) {
khint_t entry = kh_put(str2int, hash, strdup(buf), &ret);
kh_val(hash, entry) = serial;
serial++;
}
fclose(fp_list);
}
// in and out
char *fn_in = argv[optind];
char *fn_out = argv[optind + 1];
gzFile fp = gzdopen(fileno(source_in(fn_in)), "r");
kseq_t *seq = kseq_init(fp);
FILE *stream_out = source_out(fn_out);
while (kseq_read(seq) >= 0) {
char seq_name[512];
sprintf(seq_name, "%s", seq->name.s);
if (strcmp(fn_list, "") != 0) {
if (kh_get(str2int, hash, seq_name) != kh_end(hash)) {
sprintf(seq_name, "%s%s", prefix, seq->name.s);
if (flag_r) {
reverse_str(seq->seq.s, seq->seq.l);
} else if (flag_c) {
complement_str(seq->seq.s, seq->seq.l);
} else {
reverse_str(seq->seq.s, seq->seq.l);
complement_str(seq->seq.s, seq->seq.l);
}
}
} else {
sprintf(seq_name, "%s%s", prefix, seq->name.s);
if (flag_r) {
reverse_str(seq->seq.s, seq->seq.l);
} else if (flag_c) {
complement_str(seq->seq.s, seq->seq.l);
} else {
reverse_str(seq->seq.s, seq->seq.l);
complement_str(seq->seq.s, seq->seq.l);
}
}
fprintf(stream_out, ">%s\n", seq_name);
for (int i = 0; i < seq->seq.l; i++) {
if (line != 0 && i != 0 && (i % line) == 0) {
fputc('\n', stream_out);
}
fputc(seq->seq.s[i], stream_out);
}
fputc('\n', stream_out);
}
kseq_destroy(seq);
gzclose(fp);
if (strcmp(fn_out, "stdout") != 0) {
fclose(stream_out);
}
return 0;
}
int fa_one(int argc, char *argv[]) {
int option = 0, line = 80;
while ((option = getopt(argc, argv, "l:")) != -1) {
switch (option) {
case 'l':
line = atoi(optarg);
break;
default:
fprintf(stderr, "Unsupported option\n");
exit(1);
}
}
if (optind + 3 > argc) {
fprintf(stderr,
"\n"
"faops one - Extract one fa sequence\n"
"usage:\n"
" faops one [options] <in.fa> <name> <out.fa>\n"
"\n"
"options:\n"
" -l INT sequence line length [%d]\n"
"\n"
"in.fa == stdin means reading from stdin\n"
"out.fa == stdout means writing to stdout\n"
"\n",
line);
exit(1);
}
char *file_in = argv[optind];
char *name = argv[optind + 1];
char *file_out = argv[optind + 2];
gzFile fp = gzdopen(fileno(source_in(file_in)), "r");
kseq_t *seq = kseq_init(fp);
FILE *stream_out = source_out(file_out);
char seq_name[512];
while (kseq_read(seq) >= 0) {
sprintf(seq_name, "%s", seq->name.s);
if (strcmp(seq_name, name) == 0) {
fprintf(stream_out, ">%s\n", seq_name);
for (int i = 0; i < seq->seq.l; i++) {
if (line != 0 && i != 0 && (i % line) == 0) {
fputc('\n', stream_out);
}
fputc(seq->seq.s[i], stream_out);
}
fputc('\n', stream_out);
}
}
kseq_destroy(seq);
gzclose(fp);
if (strcmp(file_out, "stdout") != 0) {
fclose(stream_out);
}
return 0;
}
int fa_some(int argc, char *argv[]) {
int flag_i = 0;
int option = 0, line = 80;
while ((option = getopt(argc, argv, "il:")) != -1) {
switch (option) {
case 'i':
flag_i = 1;
break;
case 'l':
line = atoi(optarg);
break;
default:
fprintf(stderr, "Unsupported option\n");
exit(1);
}
}
if (optind + 3 > argc) {
fprintf(stderr,
"\n"
"faops some - Extract multiple fa sequences\n"
"usage:\n"
" faops some [options] <in.fa> <list.file> <out.fa>\n"
"\n"
"options:\n"
" -i Invert, output sequences not in the list\n"
" -l INT sequence line length [%d]\n"
"\n"
"in.fa == stdin means reading from stdin\n"
"out.fa == stdout means writing to stdout\n"
"\n",
line);
exit(1);
}
char *file_in = argv[optind];
char *file_list = argv[optind + 1];
char *file_out = argv[optind + 2];
gzFile fp = gzdopen(fileno(source_in(file_in)), "r");
kseq_t *seq = kseq_init(fp);
FILE *stream_out = source_out(file_out);
char seq_name[512];
// variables for hashing
// from Heng Li's replay to http://www.biostars.org/p/10353/
// and https://github.com/attractivechaos/klib/issues/49
khash_t(str2int) *hash; // the hash of list
hash = kh_init(str2int);
khint_t key; // the key
// Read list.file to a hash table
int serial = 0;// serials in list.file
{
FILE *fp_list;
if ((fp_list = fopen(file_list, "r")) == NULL) {
fprintf(stderr, "Cannot open list file [%s]\n", file_list);
exit(1);
}
int ret; // return value from hashing
int buf_size = BUFFER_SIZE;
char buf[buf_size]; // buffers for names in list.file
while (fscanf(fp_list, "%s\n", buf) == 1) {
key = kh_put(str2int, hash, strdup(buf), &ret);
kh_val(hash, key) = serial;
serial++;
}
fclose(fp_list);
}
int flag_key = 0; // check keys' exists
while (kseq_read(seq) >= 0) {
sprintf(seq_name, "%s", seq->name.s);
flag_key = (kh_get(str2int, hash, seq_name) != kh_end(hash));
// invert 0 invert 1
// key 1 1 0
// key 0 0 1
// xor
if ((!flag_key) != (!flag_i)) {
fprintf(stream_out, ">%s\n", seq_name);
for (int i = 0; i < seq->seq.l; i++) {
if (line != 0 && i != 0 && (i % line) == 0) {
fputc('\n', stream_out);
}
fputc(seq->seq.s[i], stream_out);
}
fputc('\n', stream_out);
}
}
kh_destroy(str2int, hash);
kseq_destroy(seq);
gzclose(fp);
if (strcmp(file_out, "stdout") != 0) {
fclose(stream_out);
}
return 0;
}
static void copy_kstr(kstring_t *dst, const kstring_t *src) {
if (src->l == 0) return;
if (src->l + 1 > dst->m) {
dst->m = src->l + 1;
kroundup32(dst->m);
dst->s = realloc(dst->s, dst->m);
}
dst->l = src->l;
memcpy(dst->s, src->s, src->l + 1);
}
static void copy_kseq(kseq_t *dst, const kseq_t *src) {
copy_kstr(&dst->name, &src->name);
copy_kstr(&dst->seq, &src->seq);
copy_kstr(&dst->qual, &src->qual);
copy_kstr(&dst->comment, &src->comment);
}
int fa_order(int argc, char *argv[]) {
int option = 0, line = 80;
while ((option = getopt(argc, argv, "il:")) != -1) {
switch (option) {
case 'l':
line = atoi(optarg);
break;
default:
fprintf(stderr, "Unsupported option\n");
exit(1);
}
}
if (optind + 3 > argc) {
fprintf(stderr,
"\n"
"faops order - Extract multiple fa sequences by the given order.\n"
" Consume much more memory for load all sequences in memory.\n"
"usage:\n"
" faops order [options] <in.fa> <list.file> <out.fa>\n"
"\n"
"options:\n"
" -l INT sequence line length [%d]\n"
"\n"
"in.fa == stdin means reading from stdin\n"
"out.fa == stdout means writing to stdout\n"
"\n",
line);
exit(1);
}
char *file_in = argv[optind];
char *file_list = argv[optind + 1];
char *file_out = argv[optind + 2];
gzFile fp = gzdopen(fileno(source_in(file_in)), "r");
kseq_t *seq = kseq_init(fp);
FILE *stream_out = source_out(file_out);
// variables for hashing
// from Heng Li's replay to http://www.biostars.org/p/10353/
// and https://github.com/attractivechaos/klib/issues/49
khash_t(str2int) *hash; // the hash of list
hash = kh_init(str2int);
khint_t entry; // the key-value pair
// Read list.file to a hash table
int serial = 0;// serials in list.file
{
FILE *fp_list;
if ((fp_list = fopen(file_list, "r")) == NULL) {
fprintf(stderr, "Cannot open list file [%s]\n", file_list);
exit(1);
}
int ret; // return value from hashing
int buf_size = BUFFER_SIZE;
char buf[buf_size]; // buffers for names in list.file
while (fscanf(fp_list, "%s\n", buf) == 1) {
entry = kh_put(str2int, hash, strdup(buf), &ret);
kh_val(hash, entry) = serial;
// fprintf(stderr, "Key: [%s];\tValue:[%d]\n", kh_key(hash, entry), kh_val(hash, entry));
serial++;
}
fclose(fp_list);
}
// load all sequences into buffer
kseq_t *buf_seq = 0;
buf_seq = calloc((size_t) serial, sizeof(kseq_t));
while (kseq_read(seq) >= 0) {
char seq_name[512];
sprintf(seq_name, "%s", seq->name.s);
entry = kh_get(str2int, hash, seq_name);
if (entry != kh_end(hash)) {
copy_kseq(&buf_seq[kh_val(hash, entry)], seq);
}
}
for (int idx = 0; idx < serial; ++idx) {
kseq_t *seq_l = &buf_seq[idx];
fprintf(stream_out, ">%s\n", seq_l->name.s);
for (int i = 0; i < seq_l->seq.l; i++) {
if (line != 0 && i != 0 && (i % line) == 0) {
fputc('\n', stream_out);
}
fputc(seq_l->seq.s[i], stream_out);
}
fputc('\n', stream_out);
free(seq_l->seq.s);
free(seq_l->qual.s);
free(seq_l->name.s);
}
if (buf_seq != NULL) free(buf_seq);
kh_destroy(str2int, hash);
kseq_destroy(seq);
gzclose(fp);
if (strcmp(file_out, "stdout") != 0) {
fclose(stream_out);
}
return 0;
}
int fa_replace(int argc, char *argv[]) {
int flag_s = 0;
int option = 0, line = 80;
while ((option = getopt(argc, argv, "sl:")) != -1) {
switch (option) {
case 's':
flag_s = 1;
break;
case 'l':
line = atoi(optarg);
break;
default:
fprintf(stderr, "Unsupported option\n");
exit(1);
}
}
if (optind + 3 > argc) {
fprintf(stderr,
"\n"
"faops replace - Replace headers from a FA file\n"
"usage:\n"
" faops replace [options] <in.fa> <replace.tsv> <out.fa>\n"
"\n"
"options:\n"
" -s only output sequences in the list, like `faops some`\n"
" -l INT sequence line length [%d]\n"
"\n"
"<replace.tsv> is a tab-separated file containing two fields\n"
" original_name\treplace_name\n"
"\n"
"in.fa == stdin means reading from stdin\n"
"out.fa == stdout means writing to stdout\n"
"\n",
line);
exit(1);
}
char *file_in = argv[optind];
char *file_list = argv[optind + 1];
char *file_out = argv[optind + 2];
gzFile fp = gzdopen(fileno(source_in(file_in)), "r");
kseq_t *seq = kseq_init(fp);
FILE *stream_out = source_out(file_out);
char seq_name[512];
// Read replace.tsv to a hash table
khash_t(str2str) *hash;
hash = kh_init(str2str);
{
FILE *fp_list;
if ((fp_list = fopen(file_list, "r")) == NULL) {
fprintf(stderr, "Cannot open list file [%s]\n", file_list);
exit(1);
}
int ret; // return value from hashing
int buf_size = BUFFER_SIZE;
char buf1[buf_size]; // buffers for original_name in replace.tsv
char buf2[buf_size]; // buffers for replace_name in replace.tsv
while (fscanf(fp_list, "%s\t%s\n", buf1, buf2) == 2) {
khint_t entry = kh_put(str2str, hash, strdup(buf1), &ret);
kh_val(hash, entry) = strdup(buf2);
// fprintf(stderr, "Key: [%s];\tValue:[%s]\n", kh_key(hash, entry), kh_val(hash, entry));
}
fclose(fp_list);
}
while (kseq_read(seq) >= 0) {
sprintf(seq_name, "%s", seq->name.s);
khint_t entry = kh_get(str2str, hash, seq_name);
if (entry != kh_end(hash)) {
fprintf(stream_out, ">%s\n", kh_val(hash, entry));
} else {
if (flag_s) {
continue;